What does your S3D setup look like? I remember having to do several things, in particular doing "Add Extruder" in the "Extruder" tab. I named my extruders "Left" and "Right", and set "Extruder Toolhead Index" to "Tool 0" for "Left", and "Tool 1" for "Right".

I'm guessing that you don't have the Extruder Toolhead Index set right for the 2nd extruder. "Tool 1" and "Tool 0" are meaningful to the firmware, as they correspond to the Gcode commands "T1" and "T0", respectively. So if you assigned them "Tool 1" and "Tool 2", for example, then the second would cause an error, since the Gcode command "T2" would not correspond to anything in the firmware.

I also have this vague recollection of T0 and T1 being backwards from what I expected, which I may have fixed by swapping cables around, but watch out for that possibility.

Newest version of S3D already has the option for 0 and 1 extruders built in.
This it might be the cable where it plugs into the board. I'll check that later this week
and see if that fixes the "not seeing extruder 1" issue.

Thanks for any and all help resolving only 0 extruder working.

Can say the new hot end and filament feed is a lot better old style v3b.

Wow, you were still using the v3b? I guess it was a big step above the v3a (the one with the ceramic blob) that I started out with, so not as much incentive to switch to the v4 when it first came out.

Anyway, the issue is unlikely to be a cable issue. The machine gives very little feedback to S3D, and S3D is unlikely to be querying it for functional behavior. What's probably happening is that S3D is issuing a "T1" command to get a temperature reading and getting an error back in return.

You can check this by typing "T1" on the S3D command line, to send the command directly to the printer, and see what message it gives you in response ("OK" would be the normal response---S3D would definitely balk on any command that didn't acknowledge with an "OK").

Which puts the issue in firmware. You did update the firmware for dual support? Assuming so, did you use one of the precompiled firmwares? Does it match your machine configuration? With a v3b extruder, you may have one of those transitional machines for which you'll need to be very careful about which firmware you choose.